scholarly journals A comprehensive survey on the nature of ring:ring nucleobase stacking interactions in RNA: occurrence, structural variability and classification of the associated contacts

2020 ◽  
Author(s):  
Ayush Jhunjhunwala ◽  
Zakir Ali ◽  
Sohini Bhattacharya ◽  
Antarip Halder ◽  
Abhijit Mitra ◽  
...  
Keyword(s):  
Classification System ◽  
Classification Scheme ◽  
Relative Orientation ◽  
Stacking Interactions ◽  
Automated Identification ◽  
Base Stacking ◽  
Base Pairs ◽  
Glycosidic Bonds ◽  
Comprehensive Survey

ABSTRACTThe astonishing diversity in folding patterns of RNA 3D structures is crafted by myriads of noncovalent contacts, of which base pairing and stacking are the most prominent. Although the classification scheme proposed by Leontis and Westhof (RNA (2001), 7, 499) has been widely accepted for the annotation of RNA base pairs, the absence of an unambiguous classification system for base stacks appears to be a roadblock for exploring the stacking diversity in RNA. Here we provide an unambiguous and structurally-intuitive scheme for a geometry cum topology based classification of base stacking, where a stack is essentially classified in terms of the topology of the interacting nucleobase faces and the geometry described by the relative orientation of the glycosidic bonds. For heterodimeric stacks, this generates eight basic stacking geometric families, whereas for homodimeric stacks, this generates six of those. Further annotation in terms of the identity of the bases and the region of involvement of purines (5-membered, 6-membered or both rings), leads to the enumeration of 384 distinct RNA base stacks. Based on our classification scheme, we also present an algorithm for automated identification of stacks in RNA crystal structures. Overall, the work described here is expected to greatly facilitate structure-based RNA research.

scholarly journals A Survey and Classification of Controlled Natural Languages

2014 ◽  
Vol 40 (1) ◽  
pp. 121-170 ◽  
Author(s):  
Tobias Kuhn
Keyword(s):  
Propositional Logic ◽  
Classification Scheme ◽  
General Nature ◽  
Natural Languages ◽  
Design Decisions ◽  
Controlled Natural Language ◽  
Starting Point ◽  
Comprehensive Survey ◽  
The One

What is here called controlled natural language (CNL) has traditionally been given many different names. Especially during the last four decades, a wide variety of such languages have been designed. They are applied to improve communication among humans, to improve translation, or to provide natural and intuitive representations for formal notations. Despite the apparent differences, it seems sensible to put all these languages under the same umbrella. To bring order to the variety of languages, a general classification scheme is presented here. A comprehensive survey of existing English-based CNLs is given, listing and describing 100 languages from 1930 until today. Classification of these languages reveals that they form a single scattered cloud filling the conceptual space between natural languages such as English on the one end and formal languages such as propositional logic on the other. The goal of this article is to provide a common terminology and a common model for CNL, to contribute to the understanding of their general nature, to provide a starting point for researchers interested in the area, and to help developers to make design decisions.

scholarly journals DEVELOPMENT OF THE CLASSIFICATION OF THE CYBER SECURITY AGENTS BOUNDED RATIONALITY

2019 ◽  
Vol 4 (56) ◽  
pp. 82-90
Author(s):  
O. Milov ◽  
O. Korol ◽  
V. Khvostenko
Keyword(s):  
Decision Making ◽  
Bounded Rationality ◽  
Cyber Security ◽  
Classification System ◽  
Classification Scheme ◽  
Decision Making Process ◽  
Interacting Agents ◽  
The Subject ◽  
Formal Relations

The subject are the bounded rationality agents of cyber security system. The purpose of this work is is to build a classification system for agents of a cybersecurity system with limited rationality. The tasks: consideration of the decisionmaking process by agents in cybersecurity systems, analysis of various manifestations of bounded rationality of agents of the cybersecurity system, introduction of classification features of bounded rationality, formal presentation of bounded rationality of various types, combining agents with various types of bounded rationality into a whole classification system. Results. Presents approaches to the classification of the concept of rationality in relation to cybersecurity systems. Such types of rationality are considered as strong, semi-strong, weak. Further classification of types of rationality is carried out on the basis of the place of manifestation of rationality. For this, the decision-making process in the cybersecurity system has been considered, formal relations have been introduced, which characterize its various stages. Such types of bounded rationality as informational, methodological, predictive, evaluative and conditional are considered. The ratio of the considered types of rationality is presented. Conclusion: A comparison of various types of bounded rationality, based primarily on its place in the decision-making process, made it possible to propose a classification scheme of bounded rationality characteristic of agents of the cybersecurity system. The result of the formalization of the description of bounded rationality is presented, which can be used as the basis for the development of models of behavior of interacting agents of cybersecurity systems.

scholarly journals UV Spectral Classification of B Stars

1985 ◽  
Vol 111 ◽  
pp. 411-413
Author(s):  
Janet Rountree ◽  
George Sonneborn ◽  
Robert J. Panek
Keyword(s):  
Classification System ◽  
Classification Criteria ◽  
High Dispersion ◽  
Spectral Classification ◽  
Early Type ◽  
B Stars ◽  
Dimensional Classification ◽  
Early Type Stars ◽  
Comprehensive Classification

Previous studies of ultraviolet spectral classification have been insufficient to establish a comprehensive classification system for ultraviolet spectra of early-type stars because of inadequate spectral resolution. We have initiated a new study of ultraviolet spectral classification of B stars using high-dispersion IUE archival data. High-dispersion SWP spectra of MK standards and other B stars are retrieved from the IUE archives and numerically degraded to a uniform resolution of 0.25 or 0.50 Å. The spectra (in the form of plots or photowrites) are then visually examined with the aim of setting up a two-dimensional classification matrix. We follow the method used to create the MK classification system for visual spectra. The purpose of this work is to examine the applicability of the MK system (and in particular, the set of standard stars) in the ultraviolet, and to establish classification criteria in this spectral region.

scholarly journals Bending and Base-Stacking Interactions in Double-Stranded DNA

1999 ◽  
Vol 82 (22) ◽  
pp. 4560-4563 ◽  
Author(s):  
Zhou Haijun ◽  
Zhang Yang ◽  
Ou-Yang Zhong-can
Keyword(s):  
Stacking Interactions ◽  
Base Stacking ◽  
Double Stranded Dna

System for Cross-Classification of Small Group Studies

1968 ◽  
Vol 23 (3_suppl) ◽  
pp. 1295-1304
Author(s):  
Richard Heslin ◽  
Dexter Dunphy
Keyword(s):  
Small Group ◽  
Classification System ◽  
Sufficient Information ◽  
Coding System ◽  
Similar System ◽  
Cross Classification

The article describes a method for placing information into a classification system that maximizes the flexibility in retrieval at a later time. It uses (1) a stack of edge-punched cards containing information of interest that has been punched according to (2) a coding system developed by the users. The authors have developed a classification system for the small-group field which is depicted and described in detail. It allows for coding a study on about 50 dimensions to (1) locate an article, (2) give an over-all description of the article, and (3) indicate the variables measured or discussed. Examples of uses and discussion of special features are provided to give the reader sufficient information to establish and use the system or a similar system for his own purposes.

Etiologic Classification of TIA and Minor Stroke by A-S-C-O and Causative Classification System as Compared to TOAST Reduces the Proportion of Patients Categorized as Cause Undetermined

2014 ◽  
Vol 38 (2) ◽  
pp. 121-126 ◽  
Author(s):  
Jamsheed A. Desai ◽  
Ahmad R. Abuzinadah ◽  
Oje Imoukhuede ◽  
Manya L. Bernbaum ◽  
Jayesh Modi ◽  
...  
Keyword(s):  
Classification System ◽  
Minor Stroke

scholarly journals Marine Network Protocols and Security Risks

2021 ◽  
Vol 1 (2) ◽  
pp. 239-251
Author(s):  
Ky Tran ◽  
Sid Keene ◽  
Erik Fretheim ◽  
Michail Tsikerdekis
Keyword(s):  
Network Protocols ◽  
Network Protocol ◽  
Identification System ◽  
Automated Identification ◽  
Security Risks ◽  
Domain Specific ◽  
Protocol Security ◽  
Challenges And Opportunities

Marine network protocols are domain-specific network protocols that aim to incorporate particular features within the specialized marine context that devices are implemented in. Devices implemented in such vessels involve critical equipment; however, limited research exists for marine network protocol security. In this paper, we provide an analysis of several marine network protocols used in today’s vessels and provide a classification of attack risks. Several protocols involve known security limitations, such as Automated Identification System (AIS) and National Marine Electronic Association (NMEA) 0183, while newer protocols, such as OneNet provide more security hardiness. We further identify several challenges and opportunities for future implementations of such protocols.

Introduction of a new AAC symbol classification system: the multidimensional quaternary symbol continuum (MQSC)

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Eliada Pampoulou ◽  
Donald R. Fuller
Keyword(s):  
Peer Review ◽  
Classification System ◽  
Augmentative And Alternative Communication ◽  
Social Issues ◽  
Content Type ◽  
Design Attributes ◽  
Wide Range ◽  
Current Classification ◽  
Symbol Classification

PurposeWhen the augmentative and alternative communication (ACC) model (Lloyd et al., 1990) was proposed, these components of symbols were not considered, nor were they contemplated when superordinate (Lloyd and Fuller, 1986) and subordinate levels (Fuller et al., 1992) of AAC symbol taxonomy were developed. The purpose of this paper is to revisit the ACC model and propose a new symbol classification system called multidimensional quaternary symbol continuum (MQSC)Design/methodology/approachThe field of AAC is evolving at a rapid rate in terms of its clinical, social, research and theoretical underpinnings. Advances in assessment and intervention methods, technology and social issues are all responsible to some degree for the significant changes that have occurred in the field of AAC over the last 30 years. For example, the number of aided symbol collections has increased almost exponentially over the past couple of decades. The proliferation of such a large variety of symbol collections represents a wide range of design attributes, physical attributes and linguistic characteristics for aided symbols and design attributes and linguistic characteristics for unaided symbols.FindingsTherefore, it may be time to revisit the AAC model and more specifically, one of its transmission processes referred to as the means to represent.Originality/valueThe focus of this theoretical paper then, is on the current classification of symbols, issues with respect to the current classification of symbols in terms of ambiguity of terminology and the evolution of symbols, and a proposal for a new means of classifying the means to represent.Peer reviewThe peer review history for this article is available at: https://publons.com/publon10.1108/JET-04-2021-0024

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